sparsify.with.hypergeometric {backbone} | R Documentation |
sparsify.with.hypergeometric
is a wrapper for sparsify()
that extracts the hypergeometric backbone described by Goldberg and Roth (2003).
It is equivalent to sparsify(escore = "hypergeometric", normalize = "none", filter = "threshold", umst = FALSE)
.
sparsify.with.hypergeometric(U, s, class = "original", narrative = FALSE)
U |
An unweighted unipartite graph, as: (1) an adjacency matrix in the form of a matrix or sparse |
s |
numeric: Sparsificiation threshold, 0 < s < 1; smaller values yield sparser graphs |
class |
string: the class of the returned backbone graph, one of c("original", "matrix", "Matrix", "igraph", "edgelist").
If "original", the backbone graph returned is of the same class as |
narrative |
boolean: TRUE if suggested text & citations should be displayed. |
An unweighted, undirected, unipartite graph of class class
.
package: Neal, Z. P. (2022). backbone: An R Package to Extract Network Backbones. PLOS ONE, 17, e0269137. doi: 10.1371/journal.pone.0269137
model: Goldberg, D. S., & Roth, F. P. (2003). Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences, 100, 4372-4376. doi: 10.1073/pnas.0735871100
U <- igraph::sbm.game(60, matrix(c(.75,.25,.25,.25,.75,.25,.25,.25,.75),3,3), c(20,20,20))
plot(U) #A hairball
sparse <- sparsify.with.hypergeometric(U, s = 0.3, narrative = TRUE)
plot(sparse) #Clearly visible communities